Rockeyes follow stealh fighters. It doesn't matter if they are fired from the player ship or from non-player ships (both enemy and friendly). I've tested this behaviour with FS2_orig.exe and the attached mission.

I haven't tested for sure, but I think that this is a change that Goober made on Jan 11. Specifically, rev 2.180.2.11 for weapons.cpp (on the stable branch at least). Perhaps that needs to be an ai_profile flag or something.

I'll leave this for Goober though, since he knows that situation far better than I do.

As for the difference from retail... yes, I'm aware of that. I thought long and hard about this change, but I classify it as a bugfix. It's a flaw in the code that Volition, by all appearances, intended to fix... but didn't, for whatever reason.

It's the same situation as the asteroid bug. Turrets fire on asteroids in retail FS1 but not retail FS2. We fixed that. Missiles ignore sensor-ghosted ships in retail FS1 but don't ignore stealth ships in retail FS2. We fixed that as well. It should stay fixed, IMO.

Did you take into account the TvT and dogfight missions that allow stealth ships when making your decision? Actually any multi player missions for that matter? If not then you may want to reconsider. With any lag it would be pretty hard to kill a stealth without the use of secondaries.

I can think of a few missions that this would effect. Both Stealth vs AWACS TvT missions. Mara Run. I can't think of which one but there is at least one dogfight that allows stealths.

Also unless it's been fixed all AI can see stealths. I've haven't had much time to test any new releases.

Rockeyes launched from computer controled ships still chase and attack stealth fighters. This happens in retail AND in bugged builds too. Only your own rockeyes don't chase stealth fighters. So, why should Alpha 2's rockeyes be better than mine?

Examples:
+ In the test mission, you can see how "Rokeye" Wing rockeyes chase Alpha 3 (ie. they are not dumbfired, the missiles turn trying to follow Alpha 3 flying path).
+ In the test mission, you can see how Beta rockeyes try to hit "Stealth Enemy" GTF Pegasus.
+ In PI MOD, in the 13th mission, where you have to fire the spying missile at the foe meeting, if you are discovered, enemy fighters fire Rockeyes at you. And I can swear that they chase you, they are not just dumbfired.

It sounds like the _best_ way to fix this would be to revert to retail behavior, and have an override in the mission or in the ai_profiles.tbl (mission overrides ai_profiles, no entry defaults to retail behavior). But, I think the best fix currently would be making the ai behavior match the player behavior. I'm indifferent either way. I think it should at least have that done before release, so I'm gonna bump this up to high priority.